Have you checked the sizes in the NC drill data?
Also, some manufacturers have different toleances for via holes and normal holes.
For example, a big european pooling PCB manufacturer (EuroCircuits) considers holes < 0.45 mm (18mil) to be via holes.
Normal holes have a tolerance of +/- 0.1mm (4mil), while their vias have a tolerance of +0.1/-0.3mm.
In addition, they use metric drills in 0.05mm steps, which are selected by rounding the NC drill size to the nearest 0.05 value.
Suppose there's a hole of 0.474mm (19mil), it gets rounded down to 0.45mm, which is considered a via, which can have a -0.3mm tolerance.
So the final hole can become 0.15mm, and still be within production spec!
Long story short: check the design specification and tolerances of your PCB supplier.